LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  using 1 OpenMP thread(s) per MPI task
# test of NB3B pair style with pair hybrid and KSpace solver

units           real
atom_style      full

bond_style      morse
angle_style     none
dihedral_style  none
improper_style  none

read_data       data.nb3b
Reading data file ...
  orthogonal box = (0 0 0) to (22.5907 22.359 23.4708)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  1400 atoms
  scanning bonds ...
  1 = max bonds/atom
  orthogonal box = (0 0 0) to (22.5907 22.359 23.4708)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  560 bonds
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     1 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.008 seconds

pair_style      hybrid/overlay nb3b/harmonic lj/cut/coul/long 10.0
pair_coeff      * * nb3b/harmonic MOH.nb3b.harmonic M O H
Reading nb3n/harmonic potential file MOH.nb3b.harmonic with DATE: 2016-07-29
pair_modify     mix arithmetic

pair_coeff      1 1 lj/cut/coul/long 0.000000903 5.264325869
pair_coeff      1 2 lj/cut/coul/long 0.000374621 4.214922978
pair_coeff      1 3 lj/cut/coul/long 0 2.632162934
pair_coeff      2 2 lj/cut/coul/long 0.155416412 3.165520088
pair_coeff      2 3 lj/cut/coul/long 0 1.582760044
pair_coeff      3 3 lj/cut/coul/long 0 0

kspace_style    ewald/disp 0.0001

neighbor        2.0 bin
neigh_modify    delay 5
special_bonds   lj/coul 0.0 0.0 1.0
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        1       
  special bond factors coul:  0        0        1       
     1 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds

thermo_style    custom step etotal ke temp pe ebond eangle edihed eimp                 evdwl ecoul elong press lx ly lz xy xz yz vol

timestep        1.0
run_style       respa 2 2 pair 1 kspace 2
Respa levels:
  1 = bond angle dihedral improper pair
  2 = kspace

thermo          50

### Minimize forces in structure ###

minimize        1.0e-06 1.0e-08 1000 10000
Switching to 'neigh_modify every 1 delay 0 check yes' setting during minimization
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:246)
  G vector = 0.26942562,   accuracy = 0.033206371
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:246)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 4 4 4
  4 neighbor lists, perpetual/occasional/extra = 4 0 0
  (1) pair nb3b/harmonic, perpetual
      attributes: full, newton on
      pair build: full/bin
      stencil: full/bin/3d
      bin: standard
  (2) pair lj/cut/coul/long, perpetual, half/full from (1)
      attributes: half, newton on, cut 12
      pair build: halffull/newton
      stencil: none
      bin: none
  (3) pair nb3b/harmonic, perpetual, copy from (1)
      attributes: full, newton on
      pair build: copy
      stencil: none
      bin: none
  (4) pair lj/cut/coul/long, perpetual, copy from (2)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
  vectors: nbox = 6, nkvec = 478
Per MPI rank memory allocation (min/avg/max) = 32.94 | 32.94 | 32.94 Mbytes
   Step         TotEng         KinEng          Temp          PotEng         E_bond        E_angle        E_dihed        E_impro         E_vdwl         E_coul         E_long         Press            Lx             Ly             Lz             Xy             Xz             Yz           Volume    
         0  -61505.991      0              0             -61505.991      198.11978      0              0              0              5426.6842     -20935.876     -46194.919      979.71007      22.5907        22.359         23.4708        0              0              0              11855.229    
         4  -61506.602      0              0             -61506.602      198.6967       0              0              0              5460.0889     -20970.345     -46195.042      1657.4306      22.5907        22.359         23.4708        0              0              0              11855.229    
Loop time of 0.148081 on 1 procs for 4 steps with 1400 atoms

99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
     -61505.9911741096  -61506.5851953497  -61506.6015316468
  Force two-norm initial, final = 17.89298 3.4090514
  Force max component initial, final = 0.75754389 0.13173679
  Final line search alpha, max atom move = 0.39456317 0.051978484
  Iterations, force evaluations = 4 8

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.12299    | 0.12299    | 0.12299    |   0.0 | 83.05
Bond    | 6.5917e-05 | 6.5917e-05 | 6.5917e-05 |   0.0 |  0.04
Kspace  | 0.024683   | 0.024683   | 0.024683   |   0.0 | 16.67
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00019678 | 0.00019678 | 0.00019678 |   0.0 |  0.13
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.0001499  |            |       |  0.10

Nlocal:           1400 ave        1400 max        1400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          10804 ave       10804 max       10804 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         596960 ave      596960 max      596960 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  1.19392e+06 ave 1.19392e+06 max 1.19392e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1193920
Ave neighs/atom = 852.8
Ave special neighs/atom = 0.8
Neighbor list builds = 0
Dangerous builds = 0

### Run NVE to equilibrate velocities ###

velocity        all create 298.0 4928459 mom yes rot yes dist gaussian

fix             1 all nve
fix             2 all temp/rescale 10 298.0 298.0 25.0 1.0

run             100
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:246)
  G vector = 0.26942562,   accuracy = 0.033206371
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:246)
Per MPI rank memory allocation (min/avg/max) = 32.56 | 32.56 | 32.56 Mbytes
   Step         TotEng         KinEng          Temp          PotEng         E_bond        E_angle        E_dihed        E_impro         E_vdwl         E_coul         E_long         Press            Lx             Ly             Lz             Xy             Xz             Yz           Volume    
         4  -60263.896      1242.7057      298           -61506.602      198.6967       0              0              0              5460.0889     -20970.345     -46195.042      6449.1478      22.5907        22.359         23.4708        0              0              0              11855.229    
        50  -58769.885      1186.4038      284.49884     -59956.289      309.92492      0              0              0              6168.8463     -20249.062     -46185.998      21737.824      22.5907        22.359         23.4708        0              0              0              11855.229    
       100  -58865.195      1242.7057      298           -60107.901      371.56165      0              0              0              6422.4017     -20716.005     -46185.86       22887.014      22.5907        22.359         23.4708        0              0              0              11855.229    
       104  -58865.333      1260.1244      302.177       -60125.458      386.24497      0              0              0              6377.369      -20705.327     -46183.745      19154.017      22.5907        22.359         23.4708        0              0              0              11855.229    
Loop time of 2.65297 on 1 procs for 100 steps with 1400 atoms

Performance: 3.257 ns/day, 7.369 hours/ns, 37.694 timesteps/s, 52.771 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.3323     | 2.3323     | 2.3323     |   0.0 | 87.91
Bond    | 0.001149   | 0.001149   | 0.001149   |   0.0 |  0.04
Kspace  | 0.27317    | 0.27317    | 0.27317    |   0.0 | 10.30
Neigh   | 0.038195   | 0.038195   | 0.038195   |   0.0 |  1.44
Comm    | 0.0046015  | 0.0046015  | 0.0046015  |   0.0 |  0.17
Output  | 6.6747e-05 | 6.6747e-05 | 6.6747e-05 |   0.0 |  0.00
Modify  | 0.0015664  | 0.0015664  | 0.0015664  |   0.0 |  0.06
Other   |            | 0.001876   |            |       |  0.07

Nlocal:           1400 ave        1400 max        1400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          10843 ave       10843 max       10843 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         595307 ave      595307 max      595307 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  1.19061e+06 ave 1.19061e+06 max 1.19061e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1190614
Ave neighs/atom = 850.43857
Ave special neighs/atom = 0.8
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:02
